Question: Best way to draw heatmap using Gfold deferentially expressed no replicate data
gravatar for lookamrita
8 days ago by
lookamrita0 wrote:

Hi, I have two sample (Control and Test) RNA seq data (Ref: Human) after analyzing the files using Star and GATK pipeline , I Have used Gfold to check the differential expression analysis. Now I have Gfold output file of differential expression analysis. I want to draw heatmap using it. There are 475 genes which are having more than 2 log2fc, I want that genes to use in heatmap from the Gfold output file. What is the best way to draw heatmap using it? New in RNA-seq. Need help. Thanks in advance

rna-seq next-gen R • 62 views
ADD COMMENTlink written 8 days ago by lookamrita0

Please see as a starting point:

Heatmap based with FPKM values

There are plenty of posts here on Biostars. Please use the search function.

ADD REPLYlink written 8 days ago by ATpoint16k

Even though I have log2fc value, shall I use FPKM only. Please see the example values and columns in my file. This is how it looks like:

Gene    GFOLD(2)    E-FDR   log2fdc 1stRPKM 2ndRPKM
7SK 3.63629 1   2.7294  0.0064312   0.0753654
A2ML1   8.08695 1   7.09134 0.00184317  0.47231
AADAC   2.57739 1   2.49758 0.108541    0.610544
AATK    2.68001 1   2.63272 0.0563924   0.34059
ABCA6   4.80114 1   4.7294  0.0358213   0.941189
ADD REPLYlink modified 8 days ago by h.mon25k • written 8 days ago by lookamrita0

You can use whatever you think is best. I linked this one for example code that you can adapt to feed in your FCs.

ADD REPLYlink written 8 days ago by ATpoint16k
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